Partitioning (clustering) of the data into `k`

clusters “around
medoids”, a more robust version of K-means.

```
pam(x, k, diss = inherits(x, "dist"),
metric = c("euclidean", "manhattan"),
medoids = NULL, stand = FALSE, cluster.only = FALSE,
do.swap = TRUE,
keep.diss = !diss && !cluster.only && n < 100,
keep.data = !diss && !cluster.only,
pamonce = FALSE, trace.lev = 0)
```

x

data matrix or data frame, or dissimilarity matrix or object,
depending on the value of the `diss`

argument.

In case of a matrix or data frame, each row corresponds to an
observation, and each column corresponds to a variable. All
variables must be numeric. Missing values (`NA`

s)
*are* allowed---as long as every pair of observations has at
least one case not missing.

In case of a dissimilarity matrix, `x`

is typically the output
of `daisy`

or `dist`

. Also a vector of
length n*(n-1)/2 is allowed (where n is the number of observations),
and will be interpreted in the same way as the output of the
above-mentioned functions. Missing values (`NA`

s) are
*not* allowed.

k

positive integer specifying the number of clusters, less than the number of observations.

diss

logical flag: if TRUE (default for `dist`

or
`dissimilarity`

objects), then `x`

will be considered as a
dissimilarity matrix. If FALSE, then `x`

will be considered as
a matrix of observations by variables.

metric

character string specifying the metric to be used for calculating
dissimilarities between observations.
The currently available options are "euclidean" and
"manhattan". Euclidean distances are root sum-of-squares of
differences, and manhattan distances are the sum of absolute
differences. If `x`

is already a dissimilarity matrix, then
this argument will be ignored.

medoids

NULL (default) or length-`k`

vector of integer
indices (in `1:n`

) specifying initial medoids instead of using
the ‘*build*’ algorithm.

stand

logical; if true, the measurements in `x`

are
standardized before calculating the dissimilarities. Measurements
are standardized for each variable (column), by subtracting the
variable's mean value and dividing by the variable's mean absolute
deviation. If `x`

is already a dissimilarity matrix, then this
argument will be ignored.

cluster.only

logical; if true, only the clustering will be computed and returned, see details.

do.swap

logical indicating if the **swap** phase should
happen. The default, `TRUE`

, correspond to the
original algorithm. On the other hand, the **swap** phase is
much more computer intensive than the **build** one for large
\(n\), so can be skipped by `do.swap = FALSE`

.

keep.diss, keep.data

logicals indicating if the dissimilarities
and/or input data `x`

should be kept in the result. Setting
these to `FALSE`

can give much smaller results and hence even save
memory allocation *time*.

pamonce

logical or integer in `0:5`

specifying algorithmic
short cuts as proposed by Reynolds et al. (2006), and
Schubert and Rousseeuw (2019) see below.

trace.lev

integer specifying a trace level for printing
diagnostics during the build and swap phase of the algorithm.
Default `0`

does not print anything; higher values print
increasingly more.

an object of class `"pam"`

representing the clustering. See
`?pam.object`

for details.

The basic `pam`

algorithm is fully described in chapter 2 of
Kaufman and Rousseeuw(1990). Compared to the k-means approach in `kmeans`

, the
function `pam`

has the following features: (a) it also accepts a
dissimilarity matrix; (b) it is more robust because it minimizes a sum
of dissimilarities instead of a sum of squared euclidean distances;
(c) it provides a novel graphical display, the silhouette plot (see
`plot.partition`

) (d) it allows to select the number of clusters
using `mean(silhouette(pr)[, "sil_width"])`

on the result
`pr <- pam(..)`

, or directly its component
`pr$silinfo$avg.width`

, see also `pam.object`

.

When `cluster.only`

is true, the result is simply a (possibly
named) integer vector specifying the clustering, i.e.,
`pam(x,k, cluster.only=TRUE)`

is the same as
`pam(x,k)$clustering`

but computed more efficiently.

The `pam`

-algorithm is based on the search for `k`

representative objects or medoids among the observations of the
dataset. These observations should represent the structure of the
data. After finding a set of `k`

medoids, `k`

clusters are
constructed by assigning each observation to the nearest medoid. The
goal is to find `k`

representative objects which minimize the sum
of the dissimilarities of the observations to their closest
representative object.

By default, when `medoids`

are not specified, the algorithm first
looks for a good initial set of medoids (this is called the
**build** phase). Then it finds a local minimum for the
objective function, that is, a solution such that there is no single
switch of an observation with a medoid that will decrease the
objective (this is called the **swap** phase).

When the `medoids`

are specified, their order does *not*
matter; in general, the algorithms have been designed to not depend on
the order of the observations.

The `pamonce`

option, new in cluster 1.14.2 (Jan. 2012), has been
proposed by Matthias Studer, University of Geneva, based on the
findings by Reynolds et al. (2006) and was extended by Erich Schubert,
TU Dortmund, with the FastPAM optimizations.

The default `FALSE`

(or integer `0`

) corresponds to the
original “swap” algorithm, whereas `pamonce = 1`

(or
`TRUE`

), corresponds to the first proposal ....
and `pamonce = 2`

additionally implements the second proposal as
well.

The key ideas of FastPAM (Schubert and Rousseeuw, 2019) are implemented except for the linear approximate build as follows:

`pamonce = 3`

:reduces the runtime by a factor of O(k) by exploiting that points cannot be closest to all current medoids at the same time.

`pamonce = 4`

:additionally allows executing multiple swaps per iteration, usually reducing the number of iterations.

`pamonce = 5`

:adds minor optimizations copied from the

`pamonce = 2`

approach, and is expected to be the fastest variant.

Reynolds, A., Richards, G., de la Iglesia, B. and Rayward-Smith, V. (1992)
Clustering rules: A comparison of partitioning and hierarchical
clustering algorithms;
*Journal of Mathematical Modelling and Algorithms* **5**,
475--504. 10.1007/s10852-005-9022-1.

Erich Schubert and Peter J. Rousseeuw (2019) Faster k-Medoids Clustering: Improving the PAM, CLARA, and CLARANS Algorithms; Preprint, (https://arxiv.org/abs/1810.05691).

`agnes`

for background and references;
`pam.object`

, `clara`

, `daisy`

,
`partition.object`

, `plot.partition`

,
`dist`

.

```
# NOT RUN {
## generate 25 objects, divided into 2 clusters.
x <- rbind(cbind(rnorm(10,0,0.5), rnorm(10,0,0.5)),
cbind(rnorm(15,5,0.5), rnorm(15,5,0.5)))
pamx <- pam(x, 2)
pamx # Medoids: '7' and '25' ...
summary(pamx)
plot(pamx)
## use obs. 1 & 16 as starting medoids -- same result (typically)
(p2m <- pam(x, 2, medoids = c(1,16)))
## no _build_ *and* no _swap_ phase: just cluster all obs. around (1, 16):
p2.s <- pam(x, 2, medoids = c(1,16), do.swap = FALSE)
p2.s
p3m <- pam(x, 3, trace = 2)
## rather stupid initial medoids:
(p3m. <- pam(x, 3, medoids = 3:1, trace = 1))
# }
# NOT RUN {
pam(daisy(x, metric = "manhattan"), 2, diss = TRUE)
data(ruspini)
## Plot similar to Figure 4 in Stryuf et al (1996)
# }
# NOT RUN {
plot(pam(ruspini, 4), ask = TRUE)
# }
```

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